Assessing the genetic diversity and structure of spotted hyena (Crocuta Crocuta) populations across Africa

Abstract

The spotted hyena (Crocuta crocuta) is one of the most important species in the savannah ecosystem acting as both a predator and a scavenger yet not a lot is known about this majestic species. This study aims to address the genetic diversity, population structure and gene flow of these species across different regions of the sub-Saharan distribution. 55 whole genome and restriction site-associated sequences were analysed using Heterozygosity, PCA analysis, Admixture proportions, Phylogenetic analysis and D-statistics. The results showed that the mean heterozygosity of spotted hyena was 0.00094 (RAD-seq) and 0.0011 (WGS) ranging from 0.0006 to 0.0013. Admixture proportions and phylogenetic analyses showed three main populations clusters (western, eastern and southern) but there was also detailed structuring which showed five populations (west, northeast, eastern TanzaniaKenya, westernTanzania and southern) and D-statistics showed that there is gene flow between these populations. The spotted hyena shows highly structured clusters between the western, eastern and southern, this pattern of structure was comparable to other mammals and large carnivores in the same distribution. Although there was evidence of gene flow between these regions the western appeared more differentiation from either the eastern or southern both of which shared considerable genetic material with each other was also the western showed the lowest genetic diversity between these regions, these structures are cause by historical events and anthropogenic factors. We suggest that conservation effects must focus on fostering the exchange of genetic material from the eastern and southern regions to the western regions as a priority to avoid further differentiation.